zoe 0.0.31

A nightly library for viral genomics
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190

use crate::{
    alignment::{LocalProfiles, SharedProfiles},
    data::fasta::{FastaAA, FastaNT, FastaNTAnnot, FastaSeq},
    prelude::{
        AminoAcids, AminoAcidsView, AminoAcidsViewMut, FastQ, FastQView, FastQViewMut, Nucleotides, NucleotidesView,
        NucleotidesViewMut,
    },
};

/// A module for reading and manipulating
/// [FASTA](https://en.wikipedia.org/wiki/FASTA_format) files.
pub mod fasta;
/// A module for reading and manipulating
/// [FASTQ](https://en.wikipedia.org/wiki/FASTQ_format) files.
pub mod fastq;
/// A module for reading and manipulating
/// [SAM](https://samtools.github.io/hts-specs/SAMv1.pdf) files. Provides some
/// special-case functions used by [IRMA](https://wonder.cdc.gov/amd/flu/irma/).
pub mod sam;

/// Getter trait for structures providing read access to a header/name
pub trait HeaderReadable {
    /// Gets the header from the record.
    #[must_use]
    fn header(&self) -> &str;
}

impl HeaderReadable for FastQ {
    #[inline]
    fn header(&self) -> &str {
        &self.header
    }
}

impl HeaderReadable for FastQView<'_> {
    #[inline]
    fn header(&self) -> &str {
        self.header
    }
}

impl HeaderReadable for FastQViewMut<'_> {
    #[inline]
    fn header(&self) -> &str {
        self.header
    }
}

impl HeaderReadable for FastaSeq {
    #[inline]
    fn header(&self) -> &str {
        &self.name
    }
}

impl HeaderReadable for FastaNT {
    #[inline]
    fn header(&self) -> &str {
        &self.name
    }
}

impl HeaderReadable for FastaAA {
    #[inline]
    fn header(&self) -> &str {
        &self.name
    }
}

impl HeaderReadable for FastaNTAnnot {
    #[inline]
    fn header(&self) -> &str {
        &self.name
    }
}

/// Getter trait for structures providing read access to a sequence.
///
/// The sequence can be either nucleotides or amino acids, and is returned as a
/// byte slice.
pub trait SequenceReadable {
    /// Get the sequence from the struct as a byte slice.
    #[must_use]
    fn sequence_bytes(&self) -> &[u8];
}

impl SequenceReadable for Nucleotides {
    #[inline]
    fn sequence_bytes(&self) -> &[u8] {
        self.as_ref()
    }
}

impl SequenceReadable for NucleotidesView<'_> {
    #[inline]
    fn sequence_bytes(&self) -> &[u8] {
        self.as_ref()
    }
}

impl SequenceReadable for NucleotidesViewMut<'_> {
    #[inline]
    fn sequence_bytes(&self) -> &[u8] {
        self.as_ref()
    }
}

impl SequenceReadable for AminoAcids {
    #[inline]
    fn sequence_bytes(&self) -> &[u8] {
        self.as_ref()
    }
}

impl SequenceReadable for AminoAcidsView<'_> {
    #[inline]
    fn sequence_bytes(&self) -> &[u8] {
        self.as_ref()
    }
}

impl SequenceReadable for AminoAcidsViewMut<'_> {
    #[inline]
    fn sequence_bytes(&self) -> &[u8] {
        self.as_ref()
    }
}

impl SequenceReadable for FastQ {
    #[inline]
    fn sequence_bytes(&self) -> &[u8] {
        self.sequence.as_ref()
    }
}

impl SequenceReadable for FastQView<'_> {
    #[inline]
    fn sequence_bytes(&self) -> &[u8] {
        self.sequence.as_ref()
    }
}

impl SequenceReadable for FastQViewMut<'_> {
    #[inline]
    fn sequence_bytes(&self) -> &[u8] {
        self.sequence.as_ref()
    }
}

impl SequenceReadable for FastaSeq {
    #[inline]
    fn sequence_bytes(&self) -> &[u8] {
        self.sequence.as_ref()
    }
}

impl SequenceReadable for FastaAA {
    #[inline]
    fn sequence_bytes(&self) -> &[u8] {
        self.sequence.as_ref()
    }
}

impl SequenceReadable for FastaNT {
    #[inline]
    fn sequence_bytes(&self) -> &[u8] {
        self.sequence.as_ref()
    }
}

impl SequenceReadable for FastaNTAnnot {
    #[inline]
    fn sequence_bytes(&self) -> &[u8] {
        self.sequence.as_ref()
    }
}

impl<const M: usize, const N: usize, const O: usize, const S: usize> SequenceReadable for LocalProfiles<'_, M, N, O, S> {
    #[inline]
    fn sequence_bytes(&self) -> &[u8] {
        &self.seq
    }
}

impl<const M: usize, const N: usize, const O: usize, const S: usize> SequenceReadable for SharedProfiles<'_, M, N, O, S> {
    #[inline]
    fn sequence_bytes(&self) -> &[u8] {
        &self.seq
    }
}